Background The COVID-19 pandemic has impacted multiple aspects of daily living, including behaviors associated with occupation, transportation, and health. It is unclear how these changes to daily living have impacted physical activity and sedentary behavior. Objective In this study, we add to the growing body of research on the health impact of the COVID-19 pandemic by examining longitudinal changes in objectively measured daily physical activity and sedentary behavior among overweight or obese young adults participating in an ongoing weight loss trial in San Diego, California. Methods Data were collected from 315 overweight or obese (BMI: range 25.0-39.9 kg/m2) participants aged from 18 to 35 years between November 1, 2019, and October 30, 2020, by using the Fitbit Charge 3 (Fitbit LLC). After conducting strict filtering to find valid data on consistent wear (>10 hours per day for ≥250 days), data from 97 participants were analyzed to detect multiple structural changes in time series of physical activity and sedentary behavior. An algorithm was designed to detect multiple structural changes. This allowed for the automatic identification and dating of these changes in linear regression models with CIs. The number of breakpoints in regression models was estimated by using the Bayesian information criterion and residual sum of squares; the optimal segmentation corresponded to the lowest Bayesian information criterion and residual sum of squares. To quantify the changes in each outcome during the periods identified, linear mixed effects analyses were conducted. In terms of key demographic characteristics, the 97 participants included in our analyses did not differ from the 210 participants who were excluded. Results After the initiation of the shelter-in-place order in California on March 19, 2021, there were significant decreases in step counts (−2872 steps per day; 95% CI −2734 to −3010), light physical activity times (−41.9 minutes; 95% CI −39.5 to −44.3), and moderate-to-vigorous physical activity times (−12.2 minutes; 95% CI −10.6 to −13.8), as well as significant increases in sedentary behavior times (+52.8 minutes; 95% CI 47.0-58.5). The decreases were greater than the expected declines observed during winter holidays, and as of October 30, 2020, they have not returned to the levels observed prior to the initiation of shelter-in-place orders. Conclusions Among overweight or obese young adults, physical activity times decreased and sedentary behavior times increased concurrently with the implementation of COVID-19 mitigation strategies. The health conditions associated with a sedentary lifestyle may be additional, unintended results of the COVID-19 pandemic.